TOPSPINPLOT(XWINPLOT)

Transcription

1 Mississippi NMR Workshop TOPSPINPLOT(XWINPLOT) Easy and Simple Plotting Written by: Mike Brown Version meb Bruker South Training Center

2 Topics Covered Definitions Starting XWINPLOT Layouts Plot Limits Normal 1D and 2D plots Stacked Plots Help! 2

3 Definitions autoplot: Plot data according to Plot Editor layout (1D,2D), with the current limits and scaling plot: Open the Plot Editor (1D,2D), adjust scaling, limits etc. prnt: Print the current dataset (1D,2D,3D) exactly as it appears on the screen print: Open print dialog box (1D,2D,3D) plintfac: Plot integrals with different scaling factors (au) plot_sino: Plot spectrum, scaling depends on Signal-to-Noise (au) plot_to_file: Creates a postscript file of the desired plot (au) plotx: Plots all integral regions separately with same scaling of x axis. (au) 3

4 More Definitions plot : start with TOPSPIN plot limits plot r : use plot limits defined by layout settings plot n : use the layout without any modification xwp: For convenience of XWIN-NMR users, the command xwp is mapped to plot xwpr: For convenience of XWIN-NMR users, the command xwpr is mapped to plot -r. You can also start XWINPLOT by typing Xwinplot in the command line! 4

5 prnt prnt will plot exactly what is in the spectra window of TopSpin 5

6 prnt 6

7 print print will open the print dialog box (1D,2D,3D) 7

8 Starting Xwinplot The plot limits have been set, the scaling has been set and the layout has been set Just type xwp, plot or whichever way you want to start. On the command line. 8

9 xwp - plot Layout name (from edp) menus Icons If you type xwp (or plot) in TopSpin You will use the current layout the current plot limits and scaling 9

10 Buttons Use this to insert a title Use this to insert a 1D spectra Use this to insert a 2D spectra Use this to insert a set of stacked spectra Use this to insert parameters Use this to insert a FID Use this to insert text Use this to plot T1 and T2 datasets 10

11 Layouts You can enter the layout you want to use in edp You can start Xwinplot, and then call up a new layout Or you can create your own from scratch Or you can create a new one from one of the canned layouts. 11

12 Layouts Choose a layout here in edp Don t forget the + at the front Layouts are stored normally on windows at: C:\Bruker\TOPSPIN\plot\layouts Layouts are stored on Linux at: \opt\topspin\plot\layouts But you can store your layouts any where on any disk 12

13 Layouts Every Bruker parameter set has a layout that will usually work with that experiment. Others are available You can make up your own You can also have sub directories of your own You can name your layouts anything you want, but you must supply the.xwp extension yourself. 1D+1D+1D.xwp 1D+1D+int.xwp 1D+1D+pp.xwp 1D_BB.xwp 1D_H+info.xwp 1D_H+lf.xwp 1D_H+noint+ppp.xwp 1D_H+pp+info.xwp 1D_H+pp+lf.xwp 1D_H+pp.xwp 1D_H+zoom.xwp 1D_H.xwp 1D_noediff.xwp 1D_X+int.xwp 1D_X+nopp.xwp 1D_X+ppfile.xwp 1D_X.xwp 2D_hom.xwp 2D_inv.xwp prohump.xwp proresol.xwp t1norm.xwp 13

14 Normal 1D Layout (Proton 1D_H.xwp) 14

15 Normal 1D Layout (Proton 1D_13C.xwp) 15

16 Normal 2D Layout (2D_HOMO.xwp) Remember, a COSY is usually plotted with the same limits in F1 and F2, it s a square matrix 16

17 Stacked Plots One of the problems with Stacked plots is all of the spectra scale to each other. 17

18 Plot Limits (1D) You can set the plot limits in Topspin with the cursor, right click, and choose save display region to What ever the limits are on the display will be the new plot limits for Xwinplot. 18

19 Plot Limits (1D) Or you can choose the plot limits in Xwinplot itself You can also choose the scaling of the Spectra or the integrals in this window You can also add or change the appearance of the axis and integrals 19

20 Creating a new layout from scratch Click the new icon, this blanks the current layout 20

21 Creating a new layout from scratch Check to make sure the printer and print limits are correct 21

22 Creating a new layout from scratch Click the Title button and add the title where you want it Alignment 22

23 Creating a new layout from scratch the data set that has the title you want to use 23

24 Creating a new layout from scratch Then set the orientation, size, position and attributes (color, font etc.) Make sure you hit apply before leaving! 24

25 Creating a new layout from scratch After you have the title where and how you want it click the spectra button, insert the spectra where you want it on the plot window You can use the handles to re-size and move the spectra 25

26 Creating a new layout from scratch You can change the plot limits here Set the axes and the attributes, offset etc. from here. Plot limits in hertz Or PPM 26

27 Creating a new layout from scratch Set the axis for PPM or Hertz here Add peak picking and peak marks Add integrals and integral labels here also 27

28 Creating a new layout from scratch From here you can choose the data set And the position and dimension of the spectra window 28

29 Creating a new layout from scratch The blue cross hairs indicate the cursor position 29

30 Creating a new layout from scratch If you do a right click on the spectra window you will get this menu From here you can choose the Edit Panel Or the Edit Display Object Panel 30

31 Creating a new layout The same principles apply to the parameters or NMR text or any other object you add to the plot layout. The same things apply to 2D spectra also And you can do the same sort of things for stacked plots. And of T1/T2 plots work exactly the same. 31

32 Stacked Plots Go to the first data set of the series of sets you want to plot together, its easier if they are increasing expno s or procno s Click file and then open and navigate to the stacked plot directory Choose the layout with the most appropriate number of spectra 3 in this case 32

33 Stacked Plots The right click and choose edit navigate to the stacked tab You can set the X and Y offset if you want and the number of spectra to be used 33

34 Stacked Plots Navigate to the Data Set tab, then click Select The data set selector will open up The click edit 34

35 Stacked Plots The portfolio edit should open up in the correct data set if not, navigate to the correct one Choose which data set you want and click append after each one Then click apply and apply in the data set selector 35

36 Stacked Plots Adjust the handles, and amplitude of the spectra Add a title or parameters or offsets 36

37 Special plots Showpp 37

38 Special plots Bloch Simulator from Shape tool and NMRSIM 38

39 Help Tip of the day Complete manual 39

40 References XWINPLOT Manual TopSpin Processing Reference Guide TopSpin Automation Reference Guide 40